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mibwurrepo / Microbial-bioinformatics-introductory-course-Material-2018

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
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Input files update #1

Closed jjkoehorst closed 6 years ago

jjkoehorst commented 6 years ago

We need to test a dataset used with the current latest version of NG-Tax. Wasin might be able to provide with such a set?

microsud commented 6 years ago

@jjkoehorst Somehow I missed your comment. Now sure if providing raw sequence data is ideal here. We use the already available test data from Human microbiome project output from QIIME. Using in-house datasets processed using NG-Tax from our lab may not be possible due to obvious reasons.

jjkoehorst commented 6 years ago

Could you give me the raw data that you currently use? Have been looking at https://portal.hmpdacc.org/ but there is no easy download beside a client and not sure which datasets you specifically use.

microsud commented 6 years ago

I have used already processed biom file and use the phyloseq object. The sample size is large https://qiita.ucsd.edu/study/description/1927 The phyloseq object can be found in this repository as .RDS file.

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Could you give me the raw data that you currently use? Have been looking at https://portal.hmpdacc.org/ but there is no easy download beside a client and not sure which datasets you specifically use.

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microsud commented 6 years ago

Now updated to test data set processed using NG-Tax